Consolidate all App code into Command

[meatballhat]

What type of PR is this?

• cleanup
• feature

What this PR does / why we need it:

In addition to what is described in #1586, this change:

• adds Command.Root() method for returning the "root command" (previously what was App) which is generally used to get the "root Writer". I'd like to make this access more sugary than cCtx.Command.Root().Writer once Context and Command are collapsed 🤞🏼
• consolidates "running" to a single Run method that accepts only stdlib context.Context and a string slice like os.Args
• removes the Commands type alias for []*Command
• adds and uses tracef func for runtime tracing to aid with development, testing, and debugging
• modifies many (but not all!) tests to use testify/require
• moves expectFileContent from fish_test.go to cli_test.go and modifies it to use testify/require
• replaces mutated HelpName string with FullName method, which also removes the ability to customize the name used for a command in help text
• replaces global variables for some commands and flags with private functions for building copies when needed
• removes (I assume) accidentally added binary file in ./cmd/
• probably other notable things 😬 I could have been more careful. Critical feedback wanted! 🙇🏼

Which issue(s) this PR fixes:

Closes #1586